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Original Articles

Application of DNA barcoding and metabarcoding for species identification in salmon products

ORCID Icon, , , , , , & ORCID Icon show all
Pages 754-768 | Received 13 Aug 2020, Accepted 08 Dec 2020, Published online: 30 Mar 2021

References

  • Ballin NZ, Vogensen FK, Karlsson AH. 2009. Species determination - Can we detect and quantify meat adulteration? Meat Sci. 83:165–174. doi:10.1016/j.meatsci.2009.06.003.
  • Barbuto M, Galimberti A, Ferri E, Labra M, Malandra R, Galli P, Casiraghi M. 2010. DNA barcoding reveals fraudulent substitutions in shark seafood products: the Italian case of “palombo” (Mustelus spp.). Food Res Int. 43:376–381. doi:10.1016/j.foodres.2009.10.009.
  • Bertolini F, Ghionda MC, D’Alessandro E, Geraci C, Chiofalo V, Fontanesi L. 2015. A next generation semiconductor based sequencing approach for the identification of meat species in DNA mixtures. Plos One. 29:e0121701.
  • Bokulich NA, Subramanian S, Faith JJ, Gevers D, Gordon JI, Knight R, Mills DA, Caporaso JG. 2013. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing. Nat Methods. 10:57–59. doi:10.1038/nmeth.2276.
  • Briski E, Cristescu M, Bailey S, MacIsaac H. 2011. Use of DNA bacoding to detect invertebrate invasive species from diapausing eggs. Biol Invasions. 13:1325–1340. doi:10.1007/s10530-010-9892-7.
  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Pena AG, Goodrich JK, Gordon JI, et al. 2010. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 7:335–336. doi:10.1038/nmeth.f.303.
  • Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, Fierer N, Knight R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proc Natl Acad Sci U S A. 108:4516–4522. doi:10.1073/pnas.1000080107.
  • Casiraghi M, Labra M, Ferri E, Galimberti A, De Mattia F. 2010. DNA barcoding: a six-question tour to improve users’ awareness about the method. Brief Bioinform. 11:440–453. doi:10.1093/bib/bbq003.
  • Cline E. 2012. Marketplace substitution of Atlantic salmon for Pacific salmon in Washington State detected by DNA barcoding. Food Res Int. 45:388–393. doi:10.1016/j.foodres.2011.10.043.
  • D’Amore R, Ijaz UZ, Schirmer M, Kenny JG, Gregory R, Darby AC, Shakya M, Podar M, Quince C, Hall N. 2016. A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling. Bmc Genomics. 17:55. doi:10.1186/s12864-015-2194-9.
  • Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics. 27:2194–2200. doi:10.1093/bioinformatics/btr381.
  • Feng J, Wu Z, Xie X, Dai Z, Liu S. 2017. A real-time polymerase chain reaction method for the identification of four commercially important salmon and trout species. Mitochondrial DNA Part A. 28:104–111. doi:10.3109/19401736.2015.1111346.
  • Feng Y, Li Q, Kong L, Zheng X. 2011. DNA barcoding and phylogenetic analysis of Pectinidae (Mollusca: bivalvia) based on mitochondrial CO I and 16S rRNA genes. Mol Biol Rep. 38:291–299. doi:10.1007/s11033-010-0107-1.
  • Fernandes TJR, Amaral JS, Mafra I. 2020. DNA barcode markers applied to seafood authentication: an updated review. Crit Rev Food Sci Nutr. 1–32. doi:10.1080/10408398.2020.1811200.
  • Fernandes TJR, Costa J, Oliveira MBPP, Mafra I. 2018. Exploiting 16S rRNA gene for the detection and quantification of fish as a potential allergenic food: A comparison of two real-time PCR approaches. Food Chem. 245:1034–1041. doi:10.1016/j.foodchem.2017.11.068.
  • Folmer O, Black M, Wr H, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial Cytochrome C oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 3:294–299.
  • Goldstein PZ, Desalle R. 2003. Calibrating phylogenetic species formation in a threatened insect using DNA from historical specimens. Mol Ecol. 12:1993–1998. doi:10.1046/j.1365-294X.2003.01860.x.
  • Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, et al. 2011. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res. 21:494–504. doi:10.1101/gr.112730.110.
  • Head S, Komori H, Lamere S, Whisenant T, Nieuwerburgh F, Salomon D, Ordoukhanian P. 2014. Library construction for next-generation sequencing: overviews and challenges. BioTechniques. 56:61–77. doi:10.2144/000114133.
  • Hellberg RS, Pollack SJ, Hanner RH. 2016. Chapter 6 - seafood species identification using DNA sequencing - Science Direct. In: Naaum AM, Hanner RH, editors. Seafood authenticity and traceability: A DNA perspective. London: Academic Press; p. 113–132.
  • Horreo JL, Fitze PS, Jiménez-Valverde A, Noriega JA, Pelaez ML. 2019. Amplification of 16S rDNA reveals important fish mislabeling in Madrid restaurants. Food Control. 96:146–150. doi:10.1016/j.foodcont.2018.09.020.
  • Kamruzzaman M. 2016. Food adulteration and authenticity. Cham, Switzerland: Springer International Publishing; p. 127–148.
  • Kappel K, Haase I, Kaeppel C, Sotelo CG, Schroeder U. 2017. Species identification in mixed tuna samples with next-generation sequencing targeting two short cytochrome b gene fragments. Food Chem. 234:212–219. doi:10.1016/j.foodchem.2017.04.178.
  • Köppel R, Zimmerli F, Breitenmoser A. 2009. Heptaplex real-time PCR for the identification and quantification of DNA from beef, pork, chicken, turkey, horse meat, sheep (mutton) and goat. Eur Food Res Technol. 230:125–133. doi:10.1007/s00217-009-1154-5.
  • Kumar S, Tamura K, Nei M. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform. 5:150–163. doi:10.1093/bib/5.2.150.
  • Lakra WS, Goswami M, Gopalakrishnan A. 2009. Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: perciformes, Sciaenidae) based on 16S rRNA and cytochrome c oxidase subunit I mitochondrial genes. Mol Biol Rep. 36:831–839. doi:10.1007/s11033-008-9252-1.
  • Lane D, Pace B, Olsen G, Stahl D, Sogin M, Pace N, Lane D, Pace B, Olsen G, Stahl D, et al. 1985. Rapid determination of 16S ribosomal sequences for phylogenetic analyses. Proc Natl Acad Sci USA. 82:6955–6959. doi:10.1073/pnas.82.20.6955.
  • Laube I, Zagon J, Spiegelberg A, Butschke A, Kroh L, Broll H. 2007. Development and design of a ‘ready-to-use’ reaction plate for a PCR-based simultaneous detection of animal species in foods. Int J Food Sci Technol. 42:9–17. doi:10.1111/j.1365-2621.2006.01154.x.
  • Li T, Su C. 2018. Authenticity identification and classification of Rhodiola species in traditional Tibetan medicine based on Fourier transform near-infrared spectroscopy and chemometrics analysis. Spectrochim Acta A Mol Biomol Spectrosc. 204:131–140. doi:10.1016/j.saa.2018.06.004.
  • Liu J, Zhang Q-H, Ma F, Zhang S-F, Zhou Q, Huang A-M. 2020. Three-step identification of infrared spectra of similar tree species to Pterocarpus santalinus covered with beeswax. J Mol Struct. 1218:128484. doi:10.1016/j.molstruc.2020.128484.
  • Magoc T, Salzberg SL. 2011. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics. 27:2957–2963. doi:10.1093/bioinformatics/btr507.
  • Minoudi S, Karaiskou N, Avgeris M, Gkagkavouzis K, Tarantili P, Triantafyllidou D, Palilis L, Avramopoulou V, Tsikliras A, Barmperis K, et al. 2020. Seafood mislabeling in Greek market using DNA barcoding. Food Control. 113:107213. doi:10.1016/j.foodcont.2020.107213.
  • Muñoz-Colmenero M, Klett-Mingo M, Díaz E, Blanco O, Martínez JL, Garcia-Vazquez E. 2015. Evolution of hake mislabeling niches in commercial markets. Food Control. 54:267–274. doi:10.1016/j.foodcont.2015.02.006.
  • Nour M, Aboud M, Ali N. 2016. Morphological identification, species composition and distribution of mosquitoes in Kosti region, White Nile State, Central Sudan. Malaysian J Med Biol Res. 3:131–142. doi:10.18034/mjmbr.v6i1.463.
  • Pal T, Malhotra N, Chanumolu SK, Chauhan RS. 2015. Next-generation sequencing (NGS) transcriptomes reveal association of multiple genes and pathways contributing to secondary metabolites accumulation in tuberous roots of Aconitum heterophyllum Wall. Planta. 242:239–258. doi:10.1007/s00425-015-2304-6.
  • Park J, Yong Lee S, An C M, Kang J-H, Kim J-H, Chai JC, Chen J, Seok Kang J, Ahn JJ, Seek Lee Y, et al. 2012. Comparative study between next generation sequencing technique and identification of microarray for species identification within blended food products. BioChip J. 6:354–361. doi:10.1007/s13206-012-6407-x.
  • Pawluczyk M, Weiss J, Links MG, Egana Aranguren M, Wilkinson MD, Egea-Cortines M. 2015. Quantitative evaluation of bias in PCR amplification and next-generation sequencing derived from metabarcoding samples. Anal Bioanal Chem. 407:1841–1848. doi:10.1007/s00216-014-8435-y.
  • Pazartzi T, Siaperopoulou S, Gubili C, Maradidou S, Loukovitis D, Chatzispyrou A, Griffiths AM, Minos G, Imsiridou A. 2019. High levels of mislabeling in shark meat – investigating patterns of species utilization with DNA barcoding in Greek retailers. Food Control. 98:179–186. doi:10.1016/j.foodcont.2018.11.019.
  • Pinol J, Mir G, Gomez-Polo P, Agusti N. 2015. Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods. Mol Ecol Resour. 15:819–830. doi:10.1111/1755-0998.12355.
  • Pinto AJ, Raskin L. 2012. PCR biases distort bacterial and archaeal community structure in pyrosequencing datasets. PLoS One. 7:e43093. doi:10.1371/journal.pone.0043093.
  • Polz MF, Cavanaugh CM. 1998. Bias in template-to-product ratios in multitemplate PCR. Appl Environ Microbiol. 64:3724–3730. doi:10.1128/AEM.64.10.3724-3730.1998.
  • Radulovici A, Archambault P, Dufresne F. 2010. DNA barcodes for marine biodiversity: moving fast forward? Diversity. 2:450–472. doi:10.3390/d2040450.
  • Ren J, Deng T, Huang W, Chen Y, Ge Y. 2017. A digital PCR method for identifying and quantifying adulteration of meat species in raw and processed food. PLoS One. 12:e0173567. doi:10.1371/journal.pone.0173567.
  • Ribani A, Schiavo G, Utzeri VJ, Bertolini F, Geraci C, Bovo S, Fontanesi L. 2018a. Application of next generation semiconductor based sequencing for species identification and analysis of within-species mitotypes useful for authentication of meat derived products. Food Control. 91:58–67. doi:10.1016/j.foodcont.2018.03.034.
  • Ribani A, Schiavo G, Utzeri VJ, Bertolini F, Geraci C, Bovo S, Fontanesi L. 2018b. Application of next generation semiconductor based sequencing for species identification in dairy products. Food Chem. 246:90–98. doi:10.1016/j.foodchem.2017.11.006.
  • Sarri C, Stamatis C, Sarafidou T, Galara I, Godosopoulos V, Kolovos M, Liakou C, Tastsoglou S, Mamuris Z. 2014. A new set of 16S rRNA universal primers for identification of animal species. Food Control. 43:35–41. doi:10.1016/j.foodcont.2014.02.036.
  • Shen Q, Feng JL, Jin RY, Xue J, Zheng ZX, Dai ZY. 2017. Phospholipidomics profiling of salmon muscle by MALDI-TOF MS. J Chin Mass Spectrom Soc. 38:211–216. doi:10.7538/zpxb.youxian.2016.0071.
  • Speranskaya AS, Khafizov K, Ayginin AA, Krinitsina AA, Omelchenko DO, Nilova MV, Severova EE, Samokhina EN, Shipulin GA, Logacheva MD. 2018. Comparative analysis of Illumina and Ion Torrent high-throughput sequencing platforms for identification of plant components in herbal teas. Food Control. 93:315–324. doi:10.1016/j.foodcont.2018.04.040.
  • Staats M, Arulandhu AJ, Gravendeel B, Holst-jensen A, Scholtens I, Peelen T, Prins TW, Kok E. 2016. Advances in DNA metabarcoding for food and wildlife forensic species identification. Anal Bioanal Chem. 408:4615–4630. doi:10.1007/s00216-016-9595-8.
  • Sultana S, Ali ME, Hossain MAM, Asing NN, Zaidul ISM. 2018. Universal mini COI barcode for the identification of fish species in processed products. Food Res Int. 105:19–28. doi:10.1016/j.foodres.2017.10.065.
  • Thongtam Na Ayudhaya P, Muangmai N, Banjongsat N, Singchat W, Janekitkarn S, Peyachoknagul S, Srikulnath K. 2017. Unveiling cryptic diversity of the anemonefish genera Amphiprion and Premnas (Perciformes: pomacentridae) in Thailand with mitochondrial DNA barcodes. Agri Nat Resour. 51:198–205. doi:10.1016/j.anres.2017.07.001.
  • Tillmar AO, Dell’Amico B, Welander J, Holmlund G. 2013. A Universal Method for Species Identification of Mammals Utilizing Next Generation Sequencing for the Analysis of DNA Mixtures. Plos One. 8:e83761..doi:10.1371/journal.pone.0083761.
  • Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN. 2005. DNA barcoding Australia’s fish species. Philos Trans R Soc Ser. B-Biol Sci. 360:1847–1857. doi:10.1098/rstb.2005.1716.
  • Xing B, Zhang Z, Sun R, Wang Y, Lin M, Wang C. 2020a. Mini-DNA barcoding for the identification of commercial fish sold in the markets along the Taiwan Strait. Food Control. 112:107143. doi:10.1016/j.foodcont.2020.107143.
  • Xing -R-R, Hu -R-R, Han J-X, Deng -T-T, Chen Y. 2020b. DNA barcoding and mini-barcoding in authenticating processed animal-derived food: A case study involving the Chinese market. Food Chem. 309:125653. doi:10.1016/j.foodchem.2019.125653.
  • Xing R-R, Wang N, Hu R-R, Zhang J-K, Han J-X, Chen Y. 2019. Application of next generation sequencing for species identification in meat and poultry products: A DNA metabarcoding approach. Food Control. 101:173–179. doi:10.1016/j.foodcont.2019.02.034.
  • Young JM, Weyrich LS, Cooper A. 2014. Forensic soil DNA analysis using high-throughput sequencing: A comparison of four molecular markers. Forensic Sci Int Genet. 13:176–184. doi:10.1016/j.fsigen.2014.07.014.
  • Zahn RJ, Silva AJ, Hellberg RS. 2020. Development of a DNA mini-barcoding protocol targeting COI for the identification of elasmobranch species in shark cartilage pills. Food Control. 109:106918. doi:10.1016/j.foodcont.2019.106918.
  • Zeng L, Wen J, Fan S, Chen Z, Xu Y, Sun Y, Chen D, Zhao J. 2018. Species identification of fish maw (Porcupinefish) products sold on the market using DNA sequencing of 16S rRNA and COI genes. Food Control. 86:159–162. doi:10.1016/j.foodcont.2017.11.031.

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